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All Journal HAYATI Journal of Biosciences Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Jurnal Gizi dan Pangan Jurnal Teknologi Dan Industri Pangan Jurnal Pengolahan Hasil Perikanan Indonesia VALENSI Jurnal Veteriner JURNAL KIMIA SAINS DAN APLIKASI BIOTROPIA - The Southeast Asian Journal of Tropical Biology Current Biochemistry Indonesian Journal of Pharmaceutical Science and Technology Agrokreatif Jurnal Ilmiah Pengabdian kepada Masyarakat Jurnal Media Gizi Indonesia (MGI) Jurnal Penelitian Pendidikan IPA (JPPIPA) Jurnal Aplikasi Teknologi Pangan QARDHUL HASAN: MEDIA PENGABDIAN KEPADA MASYARAKAT Jambura Journal of Chemistry Jurnal Entomologi Indonesia Journal of Telenursing (JOTING) JSMARTech : Journal of Smart Bioprospecting and Technology Indonesian Journal of Applied Research (IJAR) Wood Research Journal : Journal of Indonesian Wood Research Society Wood Research Journal : Journal of Indonesian Wood Research Society Jurnal Pusat Inovasi Masyarakat Jurnal Sylva Lestari JURNAL AGROINDUSTRI HALAL Jurnal Sosial dan Sains Jurnal Ilmiah Multidisiplin Nusantara Jurnal Veteriner dan Biomedis Jurnal Pengabdian Masyarakat dan Riset Pendidikan Journal of Fisheries & Marine Halal Studies and Society Buitenzorg: Journal of Tropical Science
DIMAS ANDRIANTO
Departemen Biokimia, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, Bogor 16680
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Journal : JURNAL KIMIA SAINS DAN APLIKASI

 1 
Molecular Docking of Red Betel (Piper crocatum Ruiz & Pav) Bioactive Compounds as HMG-CoA Reductase Inhibitor Bella Fatima Dora Zaelani; Mega Safithri; Dimas Andrianto
Jurnal Kimia Sains dan Aplikasi Vol 24, No 3 (2021): Volume 24 Issue 3 Year 2021
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (3142.999 KB) | DOI: 10.14710/jksa.24.3.101-107

Abstract

Cholesterol plaque buildup in artery walls occurs due to oxidation of Low-Density Lipoprotein (LDL) molecules by free radicals, which are a risk factor for coronary heart disease. Piper crocatum contains active compounds that can act as HMG-CoA reductase inhibitors, such as flavonoids, alkaloids, polyphenols, tannins, and essential oils. This study aimed to predict the potential of Piper crocatum extract and fraction compounds as HMG-CoA reductase inhibitors by investigating the ligand affinity to the HMG-CoA reductase enzyme. Ligand and receptor preparation was conducted using BIOVIA Discovery Studio Visualizer v16.1.0.15350 and AutoDock Tools v.1.5.6. Molecular docking used AutoDock Vina, while ligand visualization and receptor binding used PyMOL(TM) 1.7.4.5.Edu. The receptor used was HMG-CoA reductase (PDB code: 1HWK) with atorvastatin as a control ligand. Catechin, schisandrin B, and CHEMBL216163 had the highest inhibition with affinity energies of -7.9 kcal/mol, -8.2 kcal/mol, -8.3 kcal/mol, respectively. Amino acid residues that played a role in ligand and receptor interactions were Ser684, Asp690, Lys691, Lys692.
The potential of Myricitrin, a Flavonoid Compound in Eugenia polyantha from Indonesia, as an Antiviral Drug for SARS-Cov-2 through the Molecular Docking Analysis Syamsul Falah; Laksmi Ambarsari; Dimas Andrianto; Rini Kurniasih; Sanro Tachibana
Jurnal Kimia Sains dan Aplikasi Vol 26, No 5 (2023): Volume 26 Issue 5 Year 2023
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jksa.26.5.166-177

Abstract

A Flavonoid glycoside compound, isolated and identified from E. polyantha as myricitrin, was analyzed as a ligand for its molecular binding activity against SARS-CoV-2 protein (receptor binding domain on Spike/RBD, main protease/nsp5, EndoRNAse, RNA-dependent-RNA-polymerase/RdRp), and its receptor, ACE2, and computationally assessed via molecular docking method. This study aims to determine the potential of myricitrin in E. polyantha from Indonesia as an antiviral drug for SARS-CoV-2 through molecular docking and molecular dynamic simulation analysis. The results showed that the myricitrin had the strongest binding affinity energy towards the three important SARS-CoV-2 proteins, namely endoRNAse, main protease (3CLpro), and RdRp with ∆G values of −9.60 kcal/mol, −8.40 kcal/mol, and −8.30 kcal/mol, respectively. These values are stronger than the comparator ligands of favipiravir (−5.60 kcal/mol), atazanavir (−7.20 kcal/mol), and remdesivir (−7.70 kcal/mol). This indicated that the compound has the potential as an inhibitor against 3CLpro, endoRNAse, and RdRp of SARS-CoV-2 proteins. This result was supported by the prediction made according to the Molprobity and PASS Online web servers, which showed that myricitrin has high bioactivity potential as an enzyme inhibitor (with a score of 0.38) and antiviral (with a score of 0.704).
Co-Authors Abdjad Asih Nawangsih Abdul Aziz Abdul Razak Abdurrahman Zaky Achyar, Catellia Auliany Agus Setiyono Ahmad Faqih Aisyah Sahara Akhmad Endang Zainal Hasan Al Malik, Ahmad Fauzan Aldri Frinaldi Alexandra, Angelya Cintania Ambarsavitri, Rahmadhani Amrista Fanzani Kananga Anja Meryandini Antonius Padua Ratu Apipah Aprianti Arya Arendra Assa’addah, Habibah Aulya, Silvy AYU LESTARI Ayu Tri Nursyarah Azizah, Annisa Nur Wahida Bella Fatima Dora Zaelani Dadan Rohdiana Daeli, Gavriel Allenfar Danty Oktiana Prastiwi Dara Anggun Vachyra Dasman Lanin Dea Khalissa Anidya Destiandani, Khansa Dewi Eriyanti Dewi Kurniasih Dewi Purnamasari Dimas Andrianto Djarot Sasongko Hami Seno Dwicesaria, Maheswari Alfira Eka Wahyu Purnama Elgiani Yassifa Yulia Nur Insari Emidar Khusnu Eni Kamal Eny Ida Riyanti Eriyanti, Dewi Etik Mardliyati, Etik Eva Harlina Fahmi Hafid Faisal Rahman Falah, Samsul Febrina, Adella Fina Febrianti Firdaus, Dzikri Anfasa Firdaus, Muhamad Fajar Firmansyah, Muhammad Ade Fitrilia, Tiana Galuh Adhiyaksa Ashari Ghifari, Muhammad Nabil Gholam, Gusnia Meilin Gina Oktaviani Sabrina Hanifati, Qisthina Hardinsyah Hasanah, Ikromatul Hasim Hasim - HASIM DANURI Hasim Hasim Hazim, Naufal Wildan Heddy Julistiono Heddy Julistiono Hudayanti, Martini Husnawati, . I MADE ARTIKA Ike Agustiani Ilham Gilang Cahya Ahmada Iman, Ramadhan Nur Imelia Dewi Inawati Inawati Iqrima Basri Irfan Abdul Aziz Irsal, Riyan Alifbi Putera Istikorini, Yunik Jaka Aryantara Kuntala Jihad Waffiqa Rahmah Kusnaedi, Anggi LAKSMI AMBARSARI Latifah Kosim Darusman Latifah, Aminahtun Lestari, Ella Deffi Lukman, Zulfiqar Madyastuti, Rini Marfiana, Arila Safa Maria Bintang Mega Safithri Mhd. Ridha Muhamad Alvin Adriyan Muhammad Farhan Muhammad Irfansyah Pradika Muhammad Zulkifli Mutholaah Mutmainnah Agustiawan Umar Nabilatusyifa, Alivianisa Nabilla, Rahmah Najmah, Najmah Nayanda, Najwa Putri Nina Tri Kusumawati Noor Farikhah Haneda Noviyan Darmawan Nurliani Bermawie Nusyarah, Ayu Tri Olive Wisepti Pratama Prasetyo, Dwiandra Hadi Pratiwi, Anggita Aziz Purwanto, Ukhradiya Magharaniq Safira Putri, Oyi Candra Santoso Putri, Salsabila Yasmin Budi Qolbiyah, Syifa Ainul Qomariah Hasanah Qurrotu Ayni R. Haryo Bimo Setiarto Raden Roro Fine Ayu Putri Rafiqi, Akbar Rahmah, Sabrina Firdayani Rahman, Syabilla Aulia Raisyadikara, Fadila Rara Annisaur Rosyidah Rembrandt Rimbawan Rimbawan Rini Kurniasih, Rini Riska Susila Putri Rizki Amelia Sasqia Putri Rosyidah, Rara Annisaur Sanro Tachibana Sari, Sintia Permata Sigiro, Ria Heni Silvy Aulya Sitanggang, Rianta Faustina Siti Maesunah Gilang Maya Slamet Hamzah Sobari, M Hilmy Rifq Sri Anna Marliyati Sri Mariati Sri Wahyuni Suci Hermita Sulistiyani SULISTIYANI SULISTIYANI Sulistiyani Sulistiyani Syaefudin Syaefudin Syaefudin Syamsul Falah Syarthibi, Ahmad Syifa Khaerani Tukan, Maria Magdalena Nona Motu Ukhradiya Magharaniq Safira Purwanto Ulfah Juniarti Siregar Vina Oktovianti Walidayyin, Sekar Wangi Waras Nurcholis Widya Prarikeslan Wilujeng, Retno Winata, Grace Marlina Yudono, Nur Annisa Windi Yupi Yulianita Arifin Yusriya, Rifqi Zaelani, Bella Fatima Dora Zulfikar Muchammad Zulfikar Muhammad, Zulfikar